Contacts of the helix formed by residues 409 - 420 (chain B) in PDB entry 2PO5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 409 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407B VAL 3.4 10.3 - - - +
408B ASN* 1.3 87.8 - - - +
410B VAL* 1.3 66.7 + - + +
411B CYS 3.2 0.4 + - - -
412B ARG* 3.7 12.9 + - + +
413B GLU* 3.0 26.7 + - - +
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ASN* 4.1 11.2 - - + +
207B TYR* 3.7 24.2 - - + -
208B ARG* 3.2 41.7 - - + +
408B ASN* 3.1 11.5 + - - +
409B PRO* 1.3 82.1 - - + +
411B CYS* 1.3 60.0 + - - +
412B ARG 3.3 0.2 - - - -
413B GLU* 3.2 12.2 + - - +
414B THR* 2.8 47.7 + - - +
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Residues in contact with CYS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B CYS* 5.6 2.9 - - - -
204B ASN* 4.2 17.0 - - - -
402B SER* 4.5 5.1 + - - +
406B CYS* 3.6 5.8 - - - -
408B ASN* 3.2 33.1 + - - +
410B VAL* 1.3 77.5 - - - +
412B ARG* 1.3 57.2 + - - +
414B THR* 3.3 2.9 + - - -
415B LYS* 2.9 29.3 + - - +
999B FES 2.4 48.5 - - - -
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Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B SER* 4.5 5.5 + - - +
408B ASN 4.5 0.8 + - - +
409B PRO* 3.7 9.0 + - + +
410B VAL 3.3 0.4 - - - -
411B CYS* 1.3 78.9 - - - +
413B GLU* 1.3 77.8 + - - +
415B LYS* 3.3 24.3 + - - +
416B SER* 3.0 36.9 + - - -
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Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B TYR* 2.5 50.3 + - + +
409B PRO* 3.0 30.4 - - - +
410B VAL* 3.2 12.1 + - - +
412B ARG* 1.3 93.8 - - - +
414B THR* 1.3 61.0 + - - +
416B SER* 3.5 7.0 + - - -
417B PHE* 2.9 27.4 + - - +
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Residues in contact with THR 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B LEU* 3.6 38.6 - - + +
204B ASN* 2.6 33.1 + - - +
207B TYR* 3.7 9.0 - - + +
399B LEU* 6.1 1.8 - - + -
410B VAL* 2.8 26.8 + - - +
411B CYS* 3.6 4.3 - - - -
413B GLU* 1.3 76.2 - - - +
415B LYS* 1.3 66.5 + - - +
417B PHE* 3.1 20.5 + - - +
418B PHE* 3.3 16.4 - - + -
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Residues in contact with LYS 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ARG* 5.1 3.1 - - - +
399B LEU* 3.1 42.2 - - + +
400B THR* 3.3 29.8 - - - +
402B SER* 4.2 14.1 + - - +
411B CYS 2.9 13.5 + - - +
412B ARG* 3.3 38.6 + - - +
414B THR* 1.3 77.3 - - - +
416B SER* 1.3 63.4 + - - +
418B PHE* 3.1 5.7 + - - +
419B THR* 3.0 36.4 + - + +
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Residues in contact with SER 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B ARG* 3.0 27.1 + - - -
413B GLU* 3.7 7.9 - - - -
415B LYS* 1.3 77.0 - - - +
417B PHE* 1.3 66.3 + - - +
419B THR* 3.5 9.9 - - - -
420B SER* 2.9 41.2 + - - -
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Residues in contact with PHE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ILE* 4.2 9.0 - - + -
207B TYR* 4.1 27.4 - + + -
210B TYR* 3.9 18.8 - + + -
216B LYS* 5.5 9.2 - - + -
217B PRO* 3.6 35.7 - - + -
221B TRP* 4.0 26.7 - + + -
413B GLU 2.9 15.1 + - - +
414B THR* 3.1 12.1 + - - +
416B SER* 1.3 78.0 - - - +
418B PHE* 1.3 87.0 + + - +
420B SER* 4.4 2.5 - - - -
421B GLN* 3.0 34.0 + - - +
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Residues in contact with PHE 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ALA* 4.3 0.7 - - + -
203B LEU* 4.1 28.9 - - + -
206B ILE* 4.2 16.4 - - + -
221B TRP* 4.3 10.7 - + + +
222B SER* 3.9 33.0 - - - -
223B THR* 3.8 22.7 - - + -
394B LEU* 3.5 23.2 - - - +
395B CYS* 4.5 6.3 - - + -
399B LEU* 4.6 9.2 - - + -
414B THR* 3.3 37.4 + - + -
415B LYS 3.1 6.0 + - - +
417B PHE* 1.3 102.6 - + - +
419B THR* 1.3 65.2 + - - +
420B SER 3.2 2.3 + - - -
421B GLN* 3.4 18.4 + - - +
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Residues in contact with THR 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B LEU* 3.6 19.7 - - - +
395B CYS* 3.7 24.0 - - - -
400B THR* 4.1 18.4 - - + -
415B LYS* 3.0 26.6 + - + +
416B SER* 3.5 10.7 - - - -
418B PHE* 1.3 75.3 - - - +
420B SER* 1.3 63.8 + - - +
421B GLN 3.4 0.4 - - - +
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Residues in contact with SER 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B SER* 2.9 30.2 + - - -
417B PHE* 4.4 2.9 - - - -
419B THR* 1.3 79.9 + - - +
421B GLN* 1.3 67.2 + - - +
422B GLN* 3.4 2.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il